Antibiotics vs. Probiotics

Germs Are Us in the current New Yorker reports on the latest developments in the intersection of traditional and alternative medicine. This is a subject where I tread lightly since my wife and I are not in total agreement about the subject. For an image, think of a see-saw. Neither of us is at one end but she sits half-way down the natural medicine end while I'm more comfortable on the other side, also not all the way to the end. 3Quarks Daily posted the link and drew a couple of positive comments so I'm passing it along to those interested in alternative or natural medicine. 

I titled this post (antibiotics versus probiotics) to underscore a growing understanding that the miracles of antibiotics are not without a downside. Most people know this but don't know exactly why. This article explains why in language understandable by any reader.

...In the past decade, however, aided by the rapidly escalating power of computer processing and by the same revolution in DNA-sequencing technology that made it possible to map our genome, another truth has emerged: while our health is certainly influenced by genes, it may be affected even more powerfully by bacteria.
We inherit every one of our genes, but we leave the womb without a single microbe. As we pass through our mother’s birth canal, we begin to attract entire colonies of bacteria. By the time a child can crawl, he has been blanketed by an enormous, unseen cloud of microorganisms—a hundred trillion or more. They are bacteria, mostly, but also viruses and fungi (including a variety of yeasts), and they come at us from all directions: other people, food, furniture, clothing, cars, buildings, trees, pets, even the air we breathe. They congregate in our digestive systems and our mouths, fill the space between our teeth, cover our skin, and line our throats. We are inhabited by as many as ten thousand bacterial species; these cells outnumber those which we consider our own by ten to one, and weigh, all told, about three pounds—the same as our brain. Together, they are referred to as our microbiome—and they play such a crucial role in our lives that scientists like Blaser have begun to reconsider what it means to be human.

Today's new word is microbiome which refers to the whole population of microbes that inhabit an organism, either plant or animal. I think of microbiome as a personalized ecosystem. (And I recall that line from Crocodile Dundee about two fleas arguing over which of them owns the dog.)

All animals have biomes. There is a cat microbiome, a dog microbiome, an alligator microbiome, and a dolphin microbiome. Earlier this summer, scientists in North Carolina State University’s Department of Poultry Science received a grant from the U.S. Department of Agriculture to study the chicken microbiome. Plants, too, need microbial communities to survive. Rhizobium, a bacterium that lives in nodules on the roots of legumes, helps its hosts carry out a series of chemical steps required to supply much of the earth’s nitrogen.

 There is a Human Microbiome Project, a spin-off the Human Genome Project, and like everything else it moving fast enough we can expect to see implications in our lifetime as well as generations to come.  By now most people understand how the overuse of antibiotics can destroy "good" bacteria as well as those causing problems. Illustrating the problem, this story toward the end of the article is too good not to mention.

Andrew Goldberg, who is the director of rhinology and sinus surgery at the U.C.S.F. Medical Center, likes to tell a story about earwax. One day in 1986, when he had just begun a residency at the University of Pittsburgh School of Medicine, a man walked into the clinic. The patient had been there many times before, always for the same reason—a chronic infection in his left ear. Stubborn ailments like that are common, though they usually occur in both ears.
“It was one of those refractory cases,” Goldberg told me recently. “The doctors had tried everything: several types of antibiotics, antifungal drops, the works. That was standard practice, and we were proud of ourselves for doing it.” Goldberg and I sat one chilly August afternoon in a coffee shop across from his office, in the Clinical Sciences Building. He spoke almost wistfully, as if recalling an antiquated practice, like bloodletting. Despite repeated treatments, the man’s ear had not improved. But on this day he walked into the clinic with a smile, and Goldberg soon saw why: the ear looked great. “I have not felt this well in years,’’ the patient said. “Do you want to know what I did?” The doctor assumed that one of the drugs had finally found its mark. “I took some wax out of my good ear and put it into my bad ear, and in a few days I was fine,” the patient said.
“I thought he was nuts,’’ Goldberg told me. He never gave the encounter another thought—until a couple of years ago, when he began to investigate the causes of those common ear infections. Goldberg explained that earwax contains many bacterial species and that antibiotics might have destroyed one or more in his bad ear. “It was actually something like a eureka moment,’’ he said, chuckling. “I realized that this patient was the perfect experiment: a good ear and a bad ear separated by a head. That guy wasn’t crazy; he was right. Clearly, he had something protecting one ear that he then transferred to the other ear. Drugs didn’t cure him. He cured himself.”

Venturing further to the edge, here is another snip.

Recently, out of desperation as much as anything else, researchers have resorted to what seems like an extreme treatment: fecal transplants. Doctors obtain fecal bacteria from healthy donors—normally family members—and place them in the patient’s intestines, usually during a colonoscopy. There have been only a few brief trials, but the results have been astounding. In one study, all thirty-four recipients were cured; these are people for whom all other approaches had failed. Other trials have reported success rates of more than eighty per cent. “There are obviously other diseases that could be susceptible to this kind of microbial therapy,’’ Lemon said; she mentioned inflammatory-bowel disease, allergies, and recurring ear infections. The hope is that someday researchers will treat bacteria with highly specific antibiotics and then rebuild our damaged ecosystem with probiotics—strains of bacteria that could act as surrogate farmers in our internal ecosystems. One study, in mice, showed that the toxic side effects of a colon-cancer drug were eased by blocking a particular bacterial enzyme. “It’s promising,’’ Lemon told me. “But we need to move very carefully to confirm the results when they look so good.

The article ends with caveats about the large and growing "natural foods" and nutritional supplements markets, neither of which has much in the way of government oversight. Consumers at this point are at the mercy of individual company reputations and industry "best practices" which are basically non-existent. It is easy to cherry-pick an avalanche of scientific data and select anything needed to peddle a product. The drug industry, supposedly regulated, has been doing it for years so it's not realistic that an unregulated industry will eschew the same practices.
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